If SCC(x) comes after SCC(NOT x) in topological order, there is no path reaching NOT x that starts at x in the condensation graph. Setting x to true will not force NOT x to be true through any chain of implications. The topological order ensures you pick values that do not propagate contradictions forward.
Any implications flow in the correct direction. This construction is both simple and correct. It always works when the formula is satisfiable.